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In [1]:
Copied!
import requests
import json
import pandas as pd
import sys
sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src")
import gwaslab as gl
import requests import json import pandas as pd import sys sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src") import gwaslab as gl
In [2]:
Copied!

In [ ]:
Copied!

In [2]:
Copied!
# Set variables object of arguments to be passed to endpoint
# Set base URL of GraphQL API endpoint
base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0004247/associations?projection=associationByEfoTrait"

# Perform POST request and check status code of response
r = requests.get(base_url)
print(r.status_code)

# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
api_response
# Set variables object of arguments to be passed to endpoint # Set base URL of GraphQL API endpoint base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0004247/associations?projection=associationByEfoTrait" # Perform POST request and check status code of response r = requests.get(base_url) print(r.status_code) # Transform API response from JSON into Python dictionary and print in console api_response = json.loads(r.text) api_response
200
Out[2]:
{'_embedded': {'associations': [{'range': None,
    'snps': [{'rsId': 'rs12532051',
      'merged': 0,
      'functionalClass': 'intron_variant',
      'lastUpdateDate': '2021-06-25T04:18:22.499+0000',
      'locations': [{'chromosomeName': '7',
        'chromosomePosition': 148109889,
        'region': {'name': '7q35'},
        '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
          'templated': True}}}],
      'genomicContexts': [{'isIntergenic': False,
        'isUpstream': False,
        'isDownstream': False,
        'distance': 0,
        'gene': {'geneName': 'CNTNAP2',
         'entrezGeneIds': [{'entrezGeneId': '26047'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000278728'},
          {'ensemblGeneId': 'ENSG00000174469'}]},
        'location': {'chromosomeName': '7',
         'chromosomePosition': 148109889,
         'region': {'name': '7q35'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
          'templated': True}}},
       {'isIntergenic': False,
        'isUpstream': False,
        'isDownstream': False,
        'distance': 0,
        'gene': {'geneName': 'CNTNAP2',
         'entrezGeneIds': [{'entrezGeneId': '26047'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000278728'},
          {'ensemblGeneId': 'ENSG00000174469'}]},
        'location': {'chromosomeName': '7',
         'chromosomePosition': 148109889,
         'region': {'name': '7q35'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
          'templated': True}}}]}],
    'loci': [{'haplotypeSnpCount': None,
      'description': 'Single variant',
      'strongestRiskAlleles': [{'riskAlleleName': 'rs12532051-C',
        'riskFrequency': '0.96',
        'genomeWide': False,
        'limitedList': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
          'templated': True}}}],
      'authorReportedGenes': [{'geneName': 'CNTNAP2',
        'entrezGeneIds': [{'entrezGeneId': '26047'}],
        'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000278728'},
         {'ensemblGeneId': 'ENSG00000174469'}]}]}],
    'riskFrequency': '0.96',
    'study': {'initialSampleSize': '90,175 European ancestry cases, 366,152 European ancestry controls',
     'gxe': False,
     'gxg': False,
     'snpCount': 8546065,
     'qualifier': None,
     'imputed': True,
     'pooled': False,
     'studyDesignComment': None,
     'accessionId': 'GCST011500',
     'fullPvalueSet': False,
     'userRequested': False,
     'platforms': [],
     'ancestries': [{'type': 'initial',
       'numberOfIndividuals': 456327,
       'ancestralGroups': [{'ancestralGroup': 'European'}],
       'countryOfOrigin': [{'majorArea': 'NR',
         'region': 'NR',
         'countryName': 'NR'}],
       'countryOfRecruitment': [{'majorArea': 'Europe',
         'region': 'Northern Europe',
         'countryName': 'U.K.'}]}],
     'diseaseTrait': {'trait': 'Gastroesophageal reflux disease, peptic ulcer disease and/or corresponding medications and treatment'},
     'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
     'replicationSampleSize': 'NA',
     'publicationInfo': {'pubmedId': '33608531',
      'publicationDate': '2021-02-19',
      'publication': 'Nat Commun',
      'title': 'GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression.',
      'author': {'fullname': 'Wu Y', 'orcid': '0000-0002-5977-1526'}}},
    'pvalueDescription': None,
    'orPerCopyNum': 1.08,
    'snpType': 'known',
    'multiSnpHaplotype': False,
    'snpInteraction': False,
    'pvalueMantissa': 1,
    'pvalueExponent': -9,
    'standardError': None,
    'pvalue': 1e-09,
    'betaNum': None,
    'betaUnit': None,
    'betaDirection': None,
    'description': None,
    '_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992'},
     'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992{?projection}',
      'templated': True},
     'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/snps'},
     'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/backgroundEfoTraits'},
     'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/study'},
     'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/efoTraits'}}},
   {'range': None,
    'snps': [{'rsId': 'rs9800013',
      'merged': 0,
      'functionalClass': 'regulatory_region_variant',
      'lastUpdateDate': '2022-08-15T15:51:09.848+0000',
      'locations': [{'chromosomeName': 'CHR_HSCHR5_5_CTG1',
        'chromosomePosition': 541908,
        'region': {'name': None},
        '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'chromosomeName': '5',
        'chromosomePosition': 541908,
        'region': {'name': '5p15.33'},
        '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}}],
      'genomicContexts': [{'isIntergenic': True,
        'isUpstream': False,
        'isDownstream': True,
        'distance': 29136,
        'gene': {'geneName': 'LOC105374607',
         'entrezGeneIds': [{'entrezGeneId': '105374607'}],
         'ensemblGeneIds': []},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 6026,
        'gene': {'geneName': 'MIR4456',
         'entrezGeneIds': [{'entrezGeneId': '100616381'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000264233'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': True,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 69971,
        'gene': {'geneName': 'EXOC3',
         'entrezGeneIds': [{'entrezGeneId': '11336'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000180104'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 68810,
        'gene': {'geneName': 'PP7080',
         'entrezGeneIds': [{'entrezGeneId': '25845'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000188242'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': False,
        'isDownstream': True,
        'distance': 70432,
        'gene': {'geneName': 'CEP72',
         'entrezGeneIds': [{'entrezGeneId': '55722'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000112877'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 6026,
        'gene': {'geneName': 'MIR4456',
         'entrezGeneIds': [{'entrezGeneId': '100616381'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000264233'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': True,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 74618,
        'gene': {'geneName': 'EXOC3',
         'entrezGeneIds': [{'entrezGeneId': '11336'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000180104'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 61016,
        'gene': {'geneName': 'SLC9A3-AS1',
         'entrezGeneIds': [{'entrezGeneId': '100288152'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000225138'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 98748,
        'gene': {'geneName': 'EXOC3-AS1',
         'entrezGeneIds': [{'entrezGeneId': '116349'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000221990'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 17459,
        'gene': {'geneName': 'SLC9A3',
         'entrezGeneIds': [{'entrezGeneId': '6550'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000066230'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': False,
        'isDownstream': True,
        'distance': 70432,
        'gene': {'geneName': 'CEP72',
         'entrezGeneIds': [{'entrezGeneId': '55722'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000112877'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': False,
        'isDownstream': True,
        'distance': 58606,
        'gene': {'geneName': 'LOC105374608',
         'entrezGeneIds': [{'entrezGeneId': '105374608'}],
         'ensemblGeneIds': []},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': False,
        'isDownstream': True,
        'distance': 60712,
        'gene': {'geneName': 'CEP72-DT',
         'entrezGeneIds': [{'entrezGeneId': '100996325'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249650'},
          {'ensemblGeneId': 'ENSG00000280978'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': True,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 68943,
        'gene': {'geneName': 'PP7080',
         'entrezGeneIds': [{'entrezGeneId': '25845'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000188242'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 61024,
        'gene': {'geneName': 'SLC9A3-AS1',
         'entrezGeneIds': [{'entrezGeneId': '100288152'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000225138'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'Ensembl',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': False,
        'isDownstream': True,
        'distance': 60261,
        'gene': {'geneName': 'CEP72-DT',
         'entrezGeneIds': [{'entrezGeneId': '100996325'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249650'},
          {'ensemblGeneId': 'ENSG00000280978'}]},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 14453,
        'gene': {'geneName': 'LOC107986395',
         'entrezGeneIds': [{'entrezGeneId': '107986395'}],
         'ensemblGeneIds': []},
        'location': {'chromosomeName': '5',
         'chromosomePosition': 541908,
         'region': {'name': '5p15.33'},
         '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
           'templated': True}}},
        'source': 'NCBI',
        'mappingMethod': 'Ensembl_pipeline',
        'isClosestGene': False,
        '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
          'templated': True}}},
       {'isIntergenic': True,
        'isUpstream': True,
        'isDownstream': False,
        'distance': 17459,
        'gene': {'geneName': 'SLC9A3',
         'entrezGeneIds': [{'entrezGeneId': '6550'}],
         'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000066230'}]},
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      'templated': True},
     'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/snps'},
     'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/backgroundEfoTraits'},
     'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/study'},
     'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/efoTraits'}}}]},
 '_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0004247/associations?projection=associationByEfoTrait'}}}
In [37]:
Copied!
for i in api_response["_embedded"]["associations"]:
    #if i is dict:
    print(i["snps"][0]["genomicContexts"][0].keys())
for i in api_response["_embedded"]["associations"]: #if i is dict: print(i["snps"][0]["genomicContexts"][0].keys())
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-37-b92f79f249ee> in <module>
      1 for i in api_response["_embedded"]["associations"]:
      2     #if i is dict:
----> 3     print(i["snps"][0]["genomicContexts"][0].keys())
      4 

IndexError: list index out of range
In [115]:
Copied!
api_response["_embedded"]["associations"]
api_response["_embedded"]["associations"]
Out[115]:
[{'range': '[1.31-1.49]',
  'snps': [{'rsId': 'rs75021220',
    'merged': 0,
    'functionalClass': 'intergenic_variant',
    'lastUpdateDate': '2021-06-24T20:23:26.532+0000',
    'locations': [{'chromosomeName': '4',
      'chromosomePosition': 110737238,
      'region': {'name': '4q25'},
      '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
        'templated': True}}}],
    'genomicContexts': [{'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 95115,
      'gene': {'geneName': 'PITX2',
       'entrezGeneIds': [{'entrezGeneId': '5308'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000164093'}]},
      'location': {'chromosomeName': '4',
       'chromosomePosition': 110737238,
       'region': {'name': '4q25'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 57165,
      'gene': {'geneName': 'LINC01438',
       'entrezGeneIds': [],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249519'}]},
      'location': {'chromosomeName': '4',
       'chromosomePosition': 110737238,
       'region': {'name': '4q25'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 95115,
      'gene': {'geneName': 'PITX2',
       'entrezGeneIds': [{'entrezGeneId': '5308'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000164093'}]},
      'location': {'chromosomeName': '4',
       'chromosomePosition': 110737238,
       'region': {'name': '4q25'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
        'templated': True}}}]}],
  'loci': [{'haplotypeSnpCount': None,
    'description': 'Single variant',
    'strongestRiskAlleles': [{'riskAlleleName': 'rs75021220-?',
      'riskFrequency': None,
      'genomeWide': False,
      'limitedList': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
        'templated': True}}}],
    'authorReportedGenes': [{'geneName': 'PITX2',
      'entrezGeneIds': [{'entrezGeneId': '5308'}],
      'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000164093'}]}]}],
  'riskFrequency': None,
  'study': {'initialSampleSize': '602 European ancestry cases, 80,613 European ancestry controls',
   'gxe': False,
   'gxg': False,
   'snpCount': None,
   'qualifier': None,
   'imputed': True,
   'pooled': False,
   'studyDesignComment': None,
   'accessionId': 'GCST003490',
   'fullPvalueSet': False,
   'userRequested': False,
   'platforms': [{'manufacturer': 'Affymetrix'}, {'manufacturer': 'Illumina'}],
   'ancestries': [{'type': 'initial',
     'numberOfIndividuals': 81215,
     'ancestralGroups': [{'ancestralGroup': 'European'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'France'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Netherlands'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Sweden'},
      {'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'}]},
    {'type': 'replication',
     'numberOfIndividuals': 19094,
     'ancestralGroups': [{'ancestralGroup': 'European'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 35900,
     'ancestralGroups': [{'ancestralGroup': 'European'},
      {'ancestralGroup': 'Hispanic or Latin American'},
      {'ancestralGroup': 'African unspecified'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]}],
   'diseaseTrait': {'trait': 'Ischemic stroke (cardioembolic)'},
   'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
   'replicationSampleSize': '579 European ancestry cases, 3,427 African unspecified, Hispanic and European ancestry cases, 18,515 European ancestry controls, 32,473 African unspecified, Hispanic and European ancestry controls',
   'publicationInfo': {'pubmedId': '27068588',
    'publicationDate': '2016-04-07',
    'publication': 'Lancet Neurol',
    'title': 'Identification of additional risk loci for stroke and small vessel disease: a meta-analysis of genome-wide association studies.',
    'author': {'fullname': 'Chauhan G', 'orcid': None}}},
  'pvalueDescription': None,
  'orPerCopyNum': 1.4,
  'snpType': 'known',
  'multiSnpHaplotype': False,
  'snpInteraction': False,
  'pvalueMantissa': 1,
  'pvalueExponent': -25,
  'standardError': None,
  'pvalue': 1e-25,
  'betaNum': None,
  'betaUnit': None,
  'betaDirection': None,
  'description': None,
  '_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372'},
   'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372{?projection}',
    'templated': True},
   'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/snps'},
   'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/backgroundEfoTraits'},
   'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/study'},
   'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/efoTraits'}}},
 {'range': '[1.11-1.23]',
  'snps': [{'rsId': 'rs7193343',
    'merged': 0,
    'functionalClass': 'intron_variant',
    'lastUpdateDate': '2021-06-24T18:30:01.511+0000',
    'locations': [{'chromosomeName': '16',
      'chromosomePosition': 72995261,
      'region': {'name': '16q22.3'},
      '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
        'templated': True}}}],
    'genomicContexts': [{'isIntergenic': False,
      'isUpstream': False,
      'isDownstream': False,
      'distance': 0,
      'gene': {'geneName': 'ZFHX3',
       'entrezGeneIds': [{'entrezGeneId': '463'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000140836'}]},
      'location': {'chromosomeName': '16',
       'chromosomePosition': 72995261,
       'region': {'name': '16q22.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 97088,
      'gene': {'geneName': 'HCCAT5',
       'entrezGeneIds': [{'entrezGeneId': '283902'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000260880'}]},
      'location': {'chromosomeName': '16',
       'chromosomePosition': 72995261,
       'region': {'name': '16q22.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
        'templated': True}}},
     {'isIntergenic': False,
      'isUpstream': False,
      'isDownstream': False,
      'distance': 0,
      'gene': {'geneName': 'ZFHX3',
       'entrezGeneIds': [{'entrezGeneId': '463'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000140836'}]},
      'location': {'chromosomeName': '16',
       'chromosomePosition': 72995261,
       'region': {'name': '16q22.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 97088,
      'gene': {'geneName': 'HCCAT5',
       'entrezGeneIds': [{'entrezGeneId': '283902'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000260880'}]},
      'location': {'chromosomeName': '16',
       'chromosomePosition': 72995261,
       'region': {'name': '16q22.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
        'templated': True}}}]}],
  'loci': [{'haplotypeSnpCount': None,
    'description': 'Single variant',
    'strongestRiskAlleles': [{'riskAlleleName': 'rs7193343-T',
      'riskFrequency': '0.174',
      'genomeWide': False,
      'limitedList': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
        'templated': True},
       'proxySnps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/NR{?projection}',
        'templated': True}}}],
    'authorReportedGenes': [{'geneName': 'ZFHX3',
      'entrezGeneIds': [{'entrezGeneId': '463'}],
      'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000140836'}]}]}],
  'riskFrequency': '0.174',
  'study': {'initialSampleSize': 'up to 3,400 European ancestry cases, up to 208 African ancestry cases, up to 118 Hispanic cases, 26,690 European ancestry controls, 3,354 African ancestry controls, 2,429 Hispanic controls',
   'gxe': False,
   'gxg': False,
   'snpCount': 15400000,
   'qualifier': 'up to',
   'imputed': True,
   'pooled': False,
   'studyDesignComment': None,
   'accessionId': 'GCST003257',
   'fullPvalueSet': False,
   'userRequested': False,
   'platforms': [{'manufacturer': 'Illumina'}],
   'ancestries': [{'type': 'initial',
     'numberOfIndividuals': 30090,
     'ancestralGroups': [{'ancestralGroup': 'European'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Sweden'},
      {'majorArea': 'Northern America', 'region': None, 'countryName': 'U.S.'},
      {'majorArea': 'Europe',
       'region': 'Eastern Europe',
       'countryName': 'Poland'},
      {'majorArea': 'Oceania',
       'region': 'Australia/New Zealand',
       'countryName': 'Australia'},
      {'majorArea': 'Northern America',
       'region': None,
       'countryName': 'Canada'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Belgium'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Germany'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'U.K.'},
      {'majorArea': 'Europe',
       'region': 'Southern Europe',
       'countryName': 'Spain'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Austria'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 3015,
     'ancestralGroups': [{'ancestralGroup': 'African American or Afro-Caribbean'},
      {'ancestralGroup': 'African unspecified'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 360,
     'ancestralGroups': [{'ancestralGroup': 'East Asian'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 277499,
     'ancestralGroups': [{'ancestralGroup': 'European'}],
     'countryOfOrigin': [{'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Sweden'},
      {'majorArea': 'Northern America', 'region': None, 'countryName': 'U.S.'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Iceland'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Netherlands'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Germany'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'U.K.'},
      {'majorArea': 'Europe',
       'region': 'Southern Europe',
       'countryName': 'Spain'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 783,
     'ancestralGroups': [{'ancestralGroup': 'Hispanic or Latin American'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 5615,
     'ancestralGroups': [{'ancestralGroup': 'South Asian'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Asia',
       'region': 'South-central Asia',
       'countryName': 'Pakistan'}]},
    {'type': 'initial',
     'numberOfIndividuals': 3562,
     'ancestralGroups': [{'ancestralGroup': 'African American or Afro-Caribbean'},
      {'ancestralGroup': 'African unspecified'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'initial',
     'numberOfIndividuals': 2547,
     'ancestralGroups': [{'ancestralGroup': 'Hispanic or Latin American'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'}]}],
   'diseaseTrait': {'trait': 'Ischemic stroke (cardioembolic)'},
   'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
   'replicationSampleSize': '98 African ancestry cases, 31 East Asian ancestry cases, 3,436 European ancestry cases, 97 Hispanic cases, 422 South Asian ancestry cases, 2,917 African ancestry controls, 329 East Asian ancestry controls, 274,063 European ancestry controls, 686 Hispanic controls, 5,193 South Asian ancestry controls',
   'publicationInfo': {'pubmedId': '26708676',
    'publicationDate': '2015-12-18',
    'publication': 'Lancet Neurol',
    'title': 'Loci associated with ischaemic stroke and its subtypes (SiGN): a genome-wide association study.',
    'author': {'fullname': 'Pulit SL', 'orcid': None}}},
  'pvalueDescription': '(CCSp)',
  'orPerCopyNum': 1.17,
  'snpType': 'known',
  'multiSnpHaplotype': False,
  'snpInteraction': False,
  'pvalueMantissa': 2,
  'pvalueExponent': -10,
  'standardError': None,
  'pvalue': 2e-10,
  'betaNum': None,
  'betaUnit': None,
  'betaDirection': None,
  'description': None,
  '_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859543'},
   'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859543{?projection}',
    'templated': True},
   'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859543/snps'},
   'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859543/backgroundEfoTraits'},
   'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859543/study'},
   'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859543/efoTraits'}}},
 {'range': '[1.30-1.45]',
  'snps': [{'rsId': 'rs2200733',
    'merged': 0,
    'functionalClass': 'intergenic_variant',
    'lastUpdateDate': '2022-09-20T16:15:31.032+0000',
    'locations': [{'chromosomeName': '4',
      'chromosomePosition': 110789013,
      'region': {'name': '4q25'},
      '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs2200733{?projection}',
        'templated': True}}}],
    'genomicContexts': [{'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 5390,
      'gene': {'geneName': 'LINC01438',
       'entrezGeneIds': [],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249519'}]},
      'location': {'chromosomeName': '4',
       'chromosomePosition': 110789013,
       'region': {'name': '4q25'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs2200733{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs2200733{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 146890,
      'gene': {'geneName': 'PITX2',
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       'region': 'Eastern Europe',
       'countryName': 'Poland'},
      {'majorArea': 'Oceania',
       'region': 'Australia/New Zealand',
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      {'majorArea': 'Northern America',
       'region': None,
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       'region': 'Western Europe',
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       'region': 'Southern Europe',
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       'countryName': 'Austria'},
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       'region': 'Northern Europe',
       'countryName': 'Iceland'},
      {'majorArea': 'Europe',
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      {'majorArea': 'Europe',
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      'limitedList': False,
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   'gxe': False,
   'gxg': False,
   'snpCount': 15400000,
   'qualifier': 'up to',
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   'studyDesignComment': None,
   'accessionId': 'GCST003260',
   'fullPvalueSet': False,
   'userRequested': False,
   'platforms': [{'manufacturer': 'Illumina'}],
   'ancestries': [{'type': 'initial',
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       'region': 'Northern Europe',
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      {'majorArea': 'Northern America', 'region': None, 'countryName': 'U.S.'},
      {'majorArea': 'Europe',
       'region': 'Eastern Europe',
       'countryName': 'Poland'},
      {'majorArea': 'Oceania',
       'region': 'Australia/New Zealand',
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      {'majorArea': 'Northern America',
       'region': None,
       'countryName': 'Canada'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Belgium'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Germany'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
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      {'majorArea': 'Europe',
       'region': 'Southern Europe',
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      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Austria'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 286,
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     'countryOfOrigin': [{'majorArea': 'NR',
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     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'replication',
     'numberOfIndividuals': 462,
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       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'NR',
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    {'type': 'replication',
     'numberOfIndividuals': 219602,
     'ancestralGroups': [{'ancestralGroup': 'European'}],
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       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Sweden'},
      {'majorArea': 'Northern America', 'region': None, 'countryName': 'U.S.'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Iceland'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
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      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Germany'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'U.K.'},
      {'majorArea': 'Europe',
       'region': 'Southern Europe',
       'countryName': 'Spain'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
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     'numberOfIndividuals': 771,
     'ancestralGroups': [{'ancestralGroup': 'Hispanic or Latin American'}],
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     'countryOfRecruitment': [{'majorArea': 'NR',
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    {'type': 'replication',
     'numberOfIndividuals': 5507,
     'ancestralGroups': [{'ancestralGroup': 'South Asian'}],
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       'region': 'NR',
       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Asia',
       'region': 'South-central Asia',
       'countryName': 'Pakistan'}]},
    {'type': 'initial',
     'numberOfIndividuals': 3735,
     'ancestralGroups': [{'ancestralGroup': 'African American or Afro-Caribbean'},
      {'ancestralGroup': 'African unspecified'}],
     'countryOfOrigin': [{'majorArea': 'NR',
       'region': 'NR',
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     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
    {'type': 'initial',
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     'ancestralGroups': [{'ancestralGroup': 'Hispanic or Latin American'}],
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       'countryName': 'NR'}],
     'countryOfRecruitment': [{'majorArea': 'Northern America',
       'region': None,
       'countryName': 'U.S.'}]}],
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   'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
   'replicationSampleSize': '47 African ancestry cases, 133 East Asian ancestry cases, 1,847 European ancestry cases, 85 Hispanic cases, 314 South Asian ancestry cases, 239 African ancestry controls, 329 East Asian ancestry controls, 217,755 European ancestry controls, 686 Hispanic controls, 5,193 South Asian ancestry stroke controls',
   'publicationInfo': {'pubmedId': '26708676',
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    'publication': 'Lancet Neurol',
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   'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859612/backgroundEfoTraits'},
   'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14859612/study'},
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 {'range': '[1.12-1.26]',
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    'strongestRiskAlleles': [{'riskAlleleName': 'rs12438353-T',
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      'limitedList': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12438353{?projection}',
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   'platforms': [{'manufacturer': 'Affymetrix'}, {'manufacturer': 'Illumina'}],
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     'numberOfIndividuals': None,
     'ancestralGroups': [{'ancestralGroup': 'European'}],
     'countryOfOrigin': [{'majorArea': 'NR',
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       'countryName': 'NR'}],
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       'countryName': 'Australia'},
      {'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
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  'betaNum': None,
  'betaUnit': None,
  'betaDirection': None,
  'description': None,
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   'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14951588/study'},
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      {'majorArea': 'Oceania',
       'region': 'Australia/New Zealand',
       'countryName': 'Australia'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Austria'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Belgium'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'France'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Germany'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Netherlands'},
      {'majorArea': 'Europe',
       'region': 'Western Europe',
       'countryName': 'Switzerland'},
      {'majorArea': 'Europe',
       'region': 'Eastern Europe',
       'countryName': 'Poland'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Denmark'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Finland'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Iceland'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Norway'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'Sweden'},
      {'majorArea': 'Europe',
       'region': 'Northern Europe',
       'countryName': 'U.K.'},
      {'majorArea': 'Europe',
       'region': 'Southern Europe',
       'countryName': 'Italy'},
      {'majorArea': 'Europe',
       'region': 'Southern Europe',
       'countryName': 'Spain'},
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   'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
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   'publicationInfo': {'pubmedId': '29531354',
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       'region': 'Australia/New Zealand',
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       'region': 'Southern Europe',
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       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 46696,
      'gene': {'geneName': 'RNU6-298P',
       'entrezGeneIds': [{'entrezGeneId': '106481273'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000212190'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 15683,
      'gene': {'geneName': 'ATAD5',
       'entrezGeneIds': [{'entrezGeneId': '79915'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000176208'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 82189,
      'gene': {'geneName': 'TEFM',
       'entrezGeneIds': [{'entrezGeneId': '79736'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000172171'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 91197,
      'gene': {'geneName': 'ADAP2',
       'entrezGeneIds': [{'entrezGeneId': '55803'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000184060'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 24239,
      'gene': {'geneName': 'SUZ12P1',
       'entrezGeneIds': [{'entrezGeneId': '440423'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000264538'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 16819,
      'gene': {'geneName': 'ATAD5',
       'entrezGeneIds': [{'entrezGeneId': '79915'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000176208'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 30815147,
       'region': {'name': '17q11.2'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}}]}],
  'loci': [{'haplotypeSnpCount': None,
    'description': 'Single variant',
    'strongestRiskAlleles': [{'riskAlleleName': 'rs564085990-A',
      'riskFrequency': None,
      'genomeWide': False,
      'limitedList': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs564085990{?projection}',
        'templated': True}}}],
    'authorReportedGenes': []}],
  'riskFrequency': '0.01004',
  'study': {'initialSampleSize': '497 Korean ancestry cases, 4,815 Korean ancestry controls',
   'gxe': False,
   'gxg': False,
   'snpCount': 7975321,
   'qualifier': None,
   'imputed': True,
   'pooled': False,
   'studyDesignComment': None,
   'accessionId': 'GCST90014127',
   'fullPvalueSet': False,
   'userRequested': False,
   'platforms': [{'manufacturer': 'Affymetrix'}],
   'ancestries': [{'type': 'initial',
     'numberOfIndividuals': 5312,
     'ancestralGroups': [{'ancestralGroup': 'East Asian'}],
     'countryOfOrigin': [],
     'countryOfRecruitment': [{'majorArea': 'Asia',
       'region': 'Eastern Asia',
       'countryName': 'Republic of Korea'}]}],
   'diseaseTrait': {'trait': 'Cardio-cerebrovascular disease in diabetes mellitus'},
   'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
   'replicationSampleSize': 'NA',
   'publicationInfo': {'pubmedId': '33632238',
    'publicationDate': '2021-02-25',
    'publication': 'J Transl Med',
    'title': 'Identification of susceptibility loci for cardiovascular disease in adults with hypertension, diabetes, and dyslipidemia.',
    'author': {'fullname': 'Song Y', 'orcid': None}}},
  'pvalueDescription': None,
  'orPerCopyNum': 3.013,
  'snpType': 'novel',
  'multiSnpHaplotype': False,
  'snpInteraction': False,
  'pvalueMantissa': 4,
  'pvalueExponent': -6,
  'standardError': None,
  'pvalue': 4e-06,
  'betaNum': None,
  'betaUnit': None,
  'betaDirection': None,
  'description': None,
  '_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852265'},
   'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852265{?projection}',
    'templated': True},
   'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852265/snps'},
   'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852265/backgroundEfoTraits'},
   'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852265/study'},
   'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852265/efoTraits'}}},
 {'range': '[2.265-5.444]',
  'snps': [{'rsId': 'rs139293840',
    'merged': 0,
    'functionalClass': 'intron_variant',
    'lastUpdateDate': '2021-06-25T04:18:10.846+0000',
    'locations': [{'chromosomeName': '17',
      'chromosomePosition': 80556559,
      'region': {'name': '17q25.3'},
      '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}}],
    'genomicContexts': [{'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 78716,
      'gene': {'geneName': 'NPTX1',
       'entrezGeneIds': [{'entrezGeneId': '4884'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000171246'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 45990,
      'gene': {'geneName': 'RPL31P7',
       'entrezGeneIds': [{'entrezGeneId': '654391'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000232083'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 45948,
      'gene': {'geneName': 'RPL31P7',
       'entrezGeneIds': [{'entrezGeneId': '654391'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000232083'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 79952,
      'gene': {'geneName': 'NPTX1',
       'entrezGeneIds': [{'entrezGeneId': '4884'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000171246'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': False,
      'isDownstream': True,
      'distance': 3543,
      'gene': {'geneName': 'LOC105371922',
       'entrezGeneIds': [{'entrezGeneId': '105371922'}],
       'ensemblGeneIds': []},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': False,
      'isUpstream': False,
      'isDownstream': False,
      'distance': 0,
      'gene': {'geneName': 'RPTOR',
       'entrezGeneIds': [{'entrezGeneId': '57521'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000141564'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 13904,
      'gene': {'geneName': 'RPL32P31',
       'entrezGeneIds': [{'entrezGeneId': '201259'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000213128'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': False,
      'isUpstream': False,
      'isDownstream': False,
      'distance': 0,
      'gene': {'geneName': 'RPTOR',
       'entrezGeneIds': [{'entrezGeneId': '57521'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000141564'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'NCBI',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}},
     {'isIntergenic': True,
      'isUpstream': True,
      'isDownstream': False,
      'distance': 13954,
      'gene': {'geneName': 'RPL32P31',
       'entrezGeneIds': [{'entrezGeneId': '201259'}],
       'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000213128'}]},
      'location': {'chromosomeName': '17',
       'chromosomePosition': 80556559,
       'region': {'name': '17q25.3'},
       '_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
         'templated': True}}},
      'source': 'Ensembl',
      'mappingMethod': 'Ensembl_pipeline',
      'isClosestGene': True,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}}]}],
  'loci': [{'haplotypeSnpCount': None,
    'description': 'Single variant',
    'strongestRiskAlleles': [{'riskAlleleName': 'rs139293840-A',
      'riskFrequency': None,
      'genomeWide': False,
      'limitedList': False,
      '_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
        'templated': True}}}],
    'authorReportedGenes': []}],
  'riskFrequency': '0.01013',
  'study': {'initialSampleSize': '497 Korean ancestry cases, 4,815 Korean ancestry controls',
   'gxe': False,
   'gxg': False,
   'snpCount': 7975321,
   'qualifier': None,
   'imputed': True,
   'pooled': False,
   'studyDesignComment': None,
   'accessionId': 'GCST90014127',
   'fullPvalueSet': False,
   'userRequested': False,
   'platforms': [{'manufacturer': 'Affymetrix'}],
   'ancestries': [{'type': 'initial',
     'numberOfIndividuals': 5312,
     'ancestralGroups': [{'ancestralGroup': 'East Asian'}],
     'countryOfOrigin': [],
     'countryOfRecruitment': [{'majorArea': 'Asia',
       'region': 'Eastern Asia',
       'countryName': 'Republic of Korea'}]}],
   'diseaseTrait': {'trait': 'Cardio-cerebrovascular disease in diabetes mellitus'},
   'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
   'replicationSampleSize': 'NA',
   'publicationInfo': {'pubmedId': '33632238',
    'publicationDate': '2021-02-25',
    'publication': 'J Transl Med',
    'title': 'Identification of susceptibility loci for cardiovascular disease in adults with hypertension, diabetes, and dyslipidemia.',
    'author': {'fullname': 'Song Y', 'orcid': None}}},
  'pvalueDescription': None,
  'orPerCopyNum': 3.511,
  'snpType': 'novel',
  'multiSnpHaplotype': False,
  'snpInteraction': False,
  'pvalueMantissa': 2,
  'pvalueExponent': -8,
  'standardError': None,
  'pvalue': 2e-08,
  'betaNum': None,
  'betaUnit': None,
  'betaDirection': None,
  'description': None,
  '_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290'},
   'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290{?projection}',
    'templated': True},
   'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/snps'},
   'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/backgroundEfoTraits'},
   'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/study'},
   'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/efoTraits'}}}]
In [3]:
Copied!
def gwascatalog_trait(efo):
    base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/"+efo+"/associations?projection=associationByEfoTrait"
    print("Start to retrieve data from GWASCatalog...")
    print(" -Requesting GWAS associations through the following GWASCatalog API...")
    print(" -api: "+ base_url)
    # Perform POST request and check status code of response
    r = requests.get(base_url)
    if r.status_code == 200:
        print(" -Retrieved data from GWASCatalog successffully ...")
    print(" -Loading json ...")
    # Transform API response from JSON into Python dictionary and print in console
    api_response = json.loads(r.text)
    records=[]
    sig_level = 5e-8
    print(" -Parsing json ...")

    records=list()
    source="NCBI"
    print("Number of associations:",len( api_response["_embedded"]["associations"]))
    for association in api_response["_embedded"]["associations"]:
        #association statistics:
        
        p=float(association["pvalue"])    
        if p < sig_level:
            try:
                function_class=association["functionalClass"] 
            except:
                function_class=None
            try:
                eaf=association["riskFrequency"]
            except:
                eaf= None
            try:
                study=association["study"]['publicationInfo']["title"]
                pubmedid=association["study"]['publicationInfo']["pubmedId"]
            except:
                study= None
                pubmedid = None
            try:
                gene = association["loci"][0]["authorReportedGenes"][0]["geneName"]
            except:
                gene = None
            try:
                OR=association["orPerCopyNum"]
            except:
                OR=None
            try:
                beta=association["betaNum"]
                se=association["standardError"]
            except:
                beta=None
                se=None    

            for snp in association["snps"]:
                if len(snp["locations"])>0:
                    for record_num in range(len(snp["locations"])):
                        if snp["locations"][record_num]["chromosomeName"] in [str(i) for i in range(1,26)]+["x","X","y","Y","mt","MT"]:
                            if len(snp["genomicContexts"])>0:
                                closegenes=set()
                                distances=set()
                                ingene=set()
                                for gene_num in range(len(snp["genomicContexts"])):
                                    if snp["genomicContexts"][gene_num]["source"]==source:
                                        distance= str(snp["genomicContexts"][gene_num]["distance"])
                                        ingene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"]
                                        if distance==0:
                                            ingene.add(ingene_name)
                                            continue
                                        if snp["genomicContexts"][gene_num]["isClosestGene"] is True:
                                            closegene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"]
                                            closegenes.add(closegene_name)
                                            distances.add(distance)

                                if len(ingene)>0:
                                    autogenes =  ",".ingene
                                else:
                                    autogenes = ",".join(closegenes)

                                row=[ snp["rsId"],
                                      snp["locations"][record_num]["chromosomeName"],
                                      snp["locations"][record_num]["chromosomePosition"],
                                      gene,
                                      autogenes,
                                      function_class,
                                      OR,
                                      beta,
                                      se,
                                      p,
                                      association["study"]["diseaseTrait"]["trait"],
                                      study,
                                      pubmedid
                                    ]
                                records.append(row)
            #rsid locations
    gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"])
    sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False)
    sigs.fix_pos(verbose=False)
    sigs.fix_chr(verbose=False)
    sigs.sort_coordinate()
    return sigs.data
def gwascatalog_trait(efo): base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/"+efo+"/associations?projection=associationByEfoTrait" print("Start to retrieve data from GWASCatalog...") print(" -Requesting GWAS associations through the following GWASCatalog API...") print(" -api: "+ base_url) # Perform POST request and check status code of response r = requests.get(base_url) if r.status_code == 200: print(" -Retrieved data from GWASCatalog successffully ...") print(" -Loading json ...") # Transform API response from JSON into Python dictionary and print in console api_response = json.loads(r.text) records=[] sig_level = 5e-8 print(" -Parsing json ...") records=list() source="NCBI" print("Number of associations:",len( api_response["_embedded"]["associations"])) for association in api_response["_embedded"]["associations"]: #association statistics: p=float(association["pvalue"]) if p < sig_level: try: function_class=association["functionalClass"] except: function_class=None try: eaf=association["riskFrequency"] except: eaf= None try: study=association["study"]['publicationInfo']["title"] pubmedid=association["study"]['publicationInfo']["pubmedId"] except: study= None pubmedid = None try: gene = association["loci"][0]["authorReportedGenes"][0]["geneName"] except: gene = None try: OR=association["orPerCopyNum"] except: OR=None try: beta=association["betaNum"] se=association["standardError"] except: beta=None se=None for snp in association["snps"]: if len(snp["locations"])>0: for record_num in range(len(snp["locations"])): if snp["locations"][record_num]["chromosomeName"] in [str(i) for i in range(1,26)]+["x","X","y","Y","mt","MT"]: if len(snp["genomicContexts"])>0: closegenes=set() distances=set() ingene=set() for gene_num in range(len(snp["genomicContexts"])): if snp["genomicContexts"][gene_num]["source"]==source: distance= str(snp["genomicContexts"][gene_num]["distance"]) ingene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"] if distance==0: ingene.add(ingene_name) continue if snp["genomicContexts"][gene_num]["isClosestGene"] is True: closegene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"] closegenes.add(closegene_name) distances.add(distance) if len(ingene)>0: autogenes = ",".ingene else: autogenes = ",".join(closegenes) row=[ snp["rsId"], snp["locations"][record_num]["chromosomeName"], snp["locations"][record_num]["chromosomePosition"], gene, autogenes, function_class, OR, beta, se, p, association["study"]["diseaseTrait"]["trait"], study, pubmedid ] records.append(row) #rsid locations gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"]) sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False) sigs.fix_pos(verbose=False) sigs.fix_chr(verbose=False) sigs.sort_coordinate() return sigs.data
In [21]:
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known = gwascatalog_trait(efo="HP_0002140")
known = gwascatalog_trait(efo="HP_0002140")
Start to retrieve data from GWASCatalog...
 -Requesting GWAS associations through the following GWASCatalog API...
 -api: https://www.ebi.ac.uk/gwas/rest/api/efoTraits/HP_0002140/associations?projection=associationByEfoTrait
 -Retrieved data from GWASCatalog successffully ...
 -Loading json ...
 -Parsing json ...
Number of associations: 429
Thu Oct 27 00:13:50 2022 Start to sort the genome coordinates...
Thu Oct 27 00:13:50 2022  -Current Dataframe shape : 198  x  13
Thu Oct 27 00:13:50 2022  -Force converting POS to integers...
Thu Oct 27 00:13:50 2022  -Sorting genome coordinates...
Thu Oct 27 00:13:50 2022 Finished sorting genome coordinates successfully!
In [5]:
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known
known
Out[5]:
SNPID CHR POS BETA SE P OR STATUS REPORT_GENENAME CLOSEST_GENENAMES TRAIT STUDY PUBMEDID
0 rs880315 1 10736809 NaN NaN 6.000000e-09 NaN 9990999 CASZ1 PEX14,LOC105376733 Ischemic stroke Multiancestry genome-wide association study of... 29531354
1 rs491203 1 15102737 NaN NaN 8.000000e-09 NaN 9990999 TMEM51 TMEM51-AS1 Acute ischemic stroke x type 2 diabetes intera... Discovery of 318 new risk loci for type 2 diab... 32541925
2 rs138364069 1 50832533 NaN NaN 7.000000e-09 3.570 9990999 FAF1 MRPS6P2,PHBP12 Ischemic stroke (large artery atherosclerosis) Genome-Wide Association Analysis of Young-Onse... 26732560
3 rs3176471 1 50973784 NaN NaN 4.000000e-08 3.700 9990999 CDKN2C FAF1,MIR4421 Ischemic stroke (large artery atherosclerosis) Genome-Wide Association Analysis of Young-Onse... 26732560
4 rs1892534 1 65640261 NaN NaN 2.000000e-16 NaN 9990999 None RN7SL854P,LOC100422694 Ischemic stroke or fibrinogen levels (pleiotropy) Multi-phenotype analyses of hemostatic traits ... 35285134
... ... ... ... ... ... ... ... ... ... ... ... ... ...
193 rs1800961 20 44413724 NaN NaN 1.000000e-10 NaN 9990999 None MIR3646,LINC01430 Ischemic stroke or fibrinogen levels (pleiotropy) Multi-phenotype analyses of hemostatic traits ... 35285134
194 rs9808651 21 39094542 NaN NaN 6.000000e-22 NaN 9990999 None RPL23AP12,LOC107985484 Ischemic stroke or fibrinogen levels (pleiotropy) Multi-phenotype analyses of hemostatic traits ... 35285134
195 rs5750823 22 39433968 NaN NaN 1.000000e-12 NaN 9990999 None SYNGR1,MGAT3 Ischemic stroke or von Willebrand factor level... Multi-phenotype analyses of hemostatic traits ... 35285134
196 rs75347843 22 50673933 NaN NaN 6.000000e-11 NaN 9990999 None ARSA,RNU6-409P Ischemic stroke or fibrinogen levels (pleiotropy) Multi-phenotype analyses of hemostatic traits ... 35285134
197 rs114209171 23 155050522 NaN NaN 7.000000e-13 1.153 9990999 F8 F8,CMC4 Thrombosis Genome-wide association analysis of self-repor... 26908601

198 rows × 13 columns

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!wget -O t2d_bbj.txt.gz http://jenger.riken.jp/14/
!wget -O t2d_bbj.txt.gz http://jenger.riken.jp/14/
--2022-10-26 23:54:33--  http://jenger.riken.jp/14/
Resolving jenger.riken.jp (jenger.riken.jp)... 134.160.84.25
Connecting to jenger.riken.jp (jenger.riken.jp)|134.160.84.25|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 274187574 (261M) [text/plain]
Saving to: ‘t2d_bbj.txt.gz’

t2d_bbj.txt.gz      100%[===================>] 261.49M  11.1MB/s    in 24s     

2022-10-26 23:55:24 (10.8 MB/s) - ‘t2d_bbj.txt.gz’ saved [274187574/274187574]

In [4]:
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Thu Oct 27 00:58:00 2022 Start to initiate from file :t2d_bbj.txt.gz
Thu Oct 27 00:58:01 2022  -Reading columns          : POS,BETA,N,REF,P,ALT,SE,Frq,Dir,SNP,CHR
Thu Oct 27 00:58:01 2022  -Renaming columns to      : POS,BETA,N,NEA,P,EA,SE,EAF,DIRECTION,SNPID,CHR
Thu Oct 27 00:58:01 2022  -Current dataframe shape  : Rows  1000000  x  11  Columns
Thu Oct 27 00:58:01 2022  -Initiating a status column ...
Thu Oct 27 00:58:01 2022  -Reordering columns to    : SNPID,CHR,POS,EA,NEA,EAF,BETA,SE,P,N,DIRECTION,STATUS
Thu Oct 27 00:58:01 2022  -NEAF is specified...
Thu Oct 27 00:58:01 2022  -Checking if 0<= NEAF <=1 ...
Thu Oct 27 00:58:01 2022  -Converted NEAF to EAF.
Thu Oct 27 00:58:01 2022  -Removed 0 variants with bad NEAF.
Thu Oct 27 00:58:01 2022 Finished loading data successfully!
In [5]:
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Thu Oct 27 00:58:01 2022 Start to check IDs...
Thu Oct 27 00:58:01 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:01 2022  -Checking if SNPID is chr:pos:ref:alt...(separator: - ,: , _)
Thu Oct 27 00:58:03 2022 Finished checking IDs successfully!
Thu Oct 27 00:58:03 2022 Start to fix chromosome notation...
Thu Oct 27 00:58:03 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:05 2022  -All CHR are already fixed...
Thu Oct 27 00:58:06 2022 Finished fixing chromosome notation successfully!
Thu Oct 27 00:58:06 2022 Start to fix basepair positions...
Thu Oct 27 00:58:06 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:07 2022  -Position upper_bound is: 250,000,000
Thu Oct 27 00:58:09 2022  -Remove outliers: 0
Thu Oct 27 00:58:09 2022  -Converted all position to datatype Int64.
Thu Oct 27 00:58:09 2022 Finished fixing basepair position successfully!
Thu Oct 27 00:58:09 2022 Start to fix alleles...
Thu Oct 27 00:58:09 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:10 2022  -Converted all bases to string datatype and UPPERCASE.
Thu Oct 27 00:58:11 2022 Finished fixing allele successfully!
Thu Oct 27 00:58:11 2022 Start sanity check for statistics ...
Thu Oct 27 00:58:11 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:11 2022  -Checking if N is Int64 and N>0 ...
Thu Oct 27 00:58:11 2022  -Removed 0 variants with bad N.
Thu Oct 27 00:58:11 2022  -Checking if 0<= EAF <=1 ...
Thu Oct 27 00:58:11 2022  -Removed 0 variants with bad EAF.
Thu Oct 27 00:58:11 2022  -Checking if MAC >=5 ...
Thu Oct 27 00:58:11 2022  -Removed 0 variants with bad MAC.
Thu Oct 27 00:58:11 2022  -Checking if 0< P <5e-300 ...
Thu Oct 27 00:58:11 2022  -Removed 0 variants with bad P.
Thu Oct 27 00:58:11 2022  -Checking if abs(BETA)<10 ...
Thu Oct 27 00:58:11 2022  -Removed 0 variants with bad BETA.
Thu Oct 27 00:58:11 2022  -Checking if SE >0 ...
Thu Oct 27 00:58:11 2022  -Removed 0 variants with bad SE.
Thu Oct 27 00:58:11 2022  -Checking STATUS...
Thu Oct 27 00:58:12 2022  -Coverting STAUTUS to category.
Thu Oct 27 00:58:12 2022  -Removed 0 variants with bad statistics in total.
Thu Oct 27 00:58:12 2022 Finished sanity check successfully!
Thu Oct 27 00:58:12 2022 Start to normalize variants...
Thu Oct 27 00:58:12 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:12 2022  -No available variants to normalize..
Thu Oct 27 00:58:12 2022 Finished normalizing variants successfully!
In [6]:
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mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
Thu Oct 27 00:58:12 2022 Start to perform liftover...
Thu Oct 27 00:58:12 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 00:58:12 2022  -CPU Cores to use : 4
Thu Oct 27 00:58:12 2022  -Performing liftover ...
Thu Oct 27 00:58:12 2022  -Creating converter : hg19 to hg38
Thu Oct 27 00:58:12 2022  -Converting variants with status code xxx0xxx :1000000...
Thu Oct 27 00:59:23 2022  -Removed unmapped variants: 619
Thu Oct 27 00:59:28 2022 Finished liftover successfully!
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mysumstats.data
mysumstats.data
Out[7]:
SNPID CHR POS EA NEA EAF BETA SE P N DIRECTION STATUS
0 1:725932_G_A 1 790552 G A 0.9960 -0.0737 0.1394 0.59700 166718 -?+- 3860099
1 1:725933_A_G 1 790553 G A 0.0040 0.0737 0.1394 0.59730 166718 +?-+ 3860099
2 1:737801_T_C 1 802421 C T 0.0051 0.0490 0.1231 0.69080 166718 +?-+ 3860099
3 1:749963_T_TAA 1 814583 TAA T 0.8374 0.0213 0.0199 0.28460 166718 -?++ 3860399
4 1:751343_T_A 1 815963 T A 0.8593 0.0172 0.0156 0.27050 166718 -?++ 3860099
... ... ... ... ... ... ... ... ... ... ... ... ...
999995 2:6347639_C_A 2 6207507 C A 0.7900 -0.0159 0.0111 0.15100 191764 ---+ 3860099
999996 2:6347694_G_C 2 6207562 G C 0.7907 -0.0151 0.0111 0.17250 191764 ---+ 3860099
999997 2:6348478_G_A 2 6208346 G A 0.7860 -0.0152 0.0111 0.17160 191764 ---+ 3860099
999998 2:6348490_G_C 2 6208358 G C 0.9985 -0.3180 0.2032 0.11750 191764 +--- 3860099
999999 2:6348754_A_C 2 6208622 C A 0.1572 0.0297 0.0126 0.01846 191764 +++- 3860099

999381 rows × 12 columns

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known = gwascatalog_trait(efo="MONDO_0005148")
known = gwascatalog_trait(efo="MONDO_0005148")
Start to retrieve data from GWASCatalog...
 -Requesting GWAS associations through the following GWASCatalog API...
 -api: https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0005148/associations?projection=associationByEfoTrait
 -Retrieved data from GWASCatalog successffully ...
 -Loading json ...
 -Parsing json ...
Number of associations: 5253
Thu Oct 27 00:35:03 2022 Start to sort the genome coordinates...
Thu Oct 27 00:35:03 2022  -Current Dataframe shape : 3939  x  13
Thu Oct 27 00:35:03 2022  -Force converting POS to integers...
Thu Oct 27 00:35:03 2022  -Sorting genome coordinates...
Thu Oct 27 00:35:03 2022 Finished sorting genome coordinates successfully!
In [24]:
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known
known
Out[24]:
SNPID CHR POS BETA SE P OR STATUS REPORT_GENENAME CLOSEST_GENENAMES TRAIT STUDY PUBMEDID
0 rs12741141 1 6609910 0.0395 0.0048 1.000000e-16 NaN 9990999 NR KLHL21,PHF13 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
1 rs11583755 1 6612669 0.0369 0.0041 1.000000e-19 NaN 9990999 NR KLHL21,PHF13 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
2 rs1010447 1 11209739 NaN NaN 2.000000e-08 NaN 9990999 MTOR RNU6-291P,ANGPTL7 Body mass index and type 2 diabetes (pairwise) Genome-wide discovery of genetic loci that unc... 33619380
3 rs4845987 1 11246222 0.0282 0.0051 3.000000e-08 NaN 9990999 NR RPL39P6,UBIAD1 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
4 rs7554251 1 11257875 0.0297 0.0045 3.000000e-11 NaN 9990999 NR RPL39P6,UBIAD1 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
... ... ... ... ... ... ... ... ... ... ... ... ... ...
3934 rs5945326 23 153634467 NaN NaN 2.000000e-12 1.140000 9990999 DUSP9 LOC105373384,DUSP9 Type 2 diabetes Genome-wide association study identifies three... 23945395
3935 rs5945326 23 153634467 NaN NaN 3.000000e-10 1.270000 9990999 DUSP9 LOC105373384,DUSP9 Type 2 diabetes Twelve type 2 diabetes susceptibility loci ide... 20581827
3936 rs5945326 23 153634467 0.1203 0.0055 8.000000e-106 NaN 9990999 None LOC105373384,DUSP9 Type 2 diabetes A cross-population atlas of genetic associatio... 34594039
3937 rs1894299 23 153643433 NaN NaN 9.000000e-58 1.130000 9990999 DUSP9 LOC105373384,RPL18AP16 Type 2 diabetes Identification of 28 new susceptibility loci f... 30718926
3938 rs1894299 23 153643433 NaN NaN 2.000000e-67 0.884338 9990999 None LOC105373384,RPL18AP16 Type 2 diabetes Large-scale genome-wide association study in a... 32514122

3939 rows × 13 columns

In [27]:
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known.to_csv("t2d_known.txt",index=None)
known.to_csv("t2d_known.txt",index=None)
In [1]:
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import requests
import json
import pandas as pd
import sys
sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src")
import gwaslab as gl
import requests import json import pandas as pd import sys sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src") import gwaslab as gl
In [2]:
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mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
             snpid="SNP",
             chrom="CHR",
             pos="POS",
             ea="ALT",
             nea="REF",
             neaf="Frq",
             beta="BETA",
             se="SE",
             p="P",
             direction="Dir",
             n="N",nrows=1000000)
mysumstats = gl.Sumstats("t2d_bbj.txt.gz", snpid="SNP", chrom="CHR", pos="POS", ea="ALT", nea="REF", neaf="Frq", beta="BETA", se="SE", p="P", direction="Dir", n="N",nrows=1000000)
Thu Oct 27 01:33:16 2022 Start to initiate from file :t2d_bbj.txt.gz
Thu Oct 27 01:33:17 2022  -Reading columns          : CHR,REF,P,POS,SE,BETA,ALT,SNP,Dir,Frq,N
Thu Oct 27 01:33:17 2022  -Renaming columns to      : CHR,NEA,P,POS,SE,BETA,EA,SNPID,DIRECTION,EAF,N
Thu Oct 27 01:33:17 2022  -Current dataframe shape  : Rows  1000000  x  11  Columns
Thu Oct 27 01:33:17 2022  -Initiating a status column ...
Thu Oct 27 01:33:17 2022  -Reordering columns to    : SNPID,CHR,POS,EA,NEA,EAF,BETA,SE,P,N,DIRECTION,STATUS
Thu Oct 27 01:33:18 2022  -NEAF is specified...
Thu Oct 27 01:33:18 2022  -Checking if 0<= NEAF <=1 ...
Thu Oct 27 01:33:18 2022  -Converted NEAF to EAF.
Thu Oct 27 01:33:18 2022  -Removed 0 variants with bad NEAF.
Thu Oct 27 01:33:18 2022 Finished loading data successfully!
In [3]:
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mysumstats.basic_check()
mysumstats.basic_check()
Thu Oct 27 01:33:18 2022 Start to check IDs...
Thu Oct 27 01:33:18 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:33:18 2022  -Checking if SNPID is chr:pos:ref:alt...(separator: - ,: , _)
Thu Oct 27 01:33:19 2022 Finished checking IDs successfully!
Thu Oct 27 01:33:19 2022 Start to fix chromosome notation...
Thu Oct 27 01:33:19 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:33:21 2022  -All CHR are already fixed...
Thu Oct 27 01:33:23 2022 Finished fixing chromosome notation successfully!
Thu Oct 27 01:33:23 2022 Start to fix basepair positions...
Thu Oct 27 01:33:23 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:33:24 2022  -Position upper_bound is: 250,000,000
Thu Oct 27 01:33:25 2022  -Remove outliers: 0
Thu Oct 27 01:33:26 2022  -Converted all position to datatype Int64.
Thu Oct 27 01:33:26 2022 Finished fixing basepair position successfully!
Thu Oct 27 01:33:26 2022 Start to fix alleles...
Thu Oct 27 01:33:26 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:33:26 2022  -Converted all bases to string datatype and UPPERCASE.
Thu Oct 27 01:33:27 2022 Finished fixing allele successfully!
Thu Oct 27 01:33:27 2022 Start sanity check for statistics ...
Thu Oct 27 01:33:27 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:33:27 2022  -Checking if N is Int64 and N>0 ...
Thu Oct 27 01:33:27 2022  -Removed 0 variants with bad N.
Thu Oct 27 01:33:27 2022  -Checking if 0<= EAF <=1 ...
Thu Oct 27 01:33:27 2022  -Removed 0 variants with bad EAF.
Thu Oct 27 01:33:27 2022  -Checking if MAC >=5 ...
Thu Oct 27 01:33:27 2022  -Removed 0 variants with bad MAC.
Thu Oct 27 01:33:27 2022  -Checking if 0< P <5e-300 ...
Thu Oct 27 01:33:28 2022  -Removed 0 variants with bad P.
Thu Oct 27 01:33:28 2022  -Checking if abs(BETA)<10 ...
Thu Oct 27 01:33:28 2022  -Removed 0 variants with bad BETA.
Thu Oct 27 01:33:28 2022  -Checking if SE >0 ...
Thu Oct 27 01:33:28 2022  -Removed 0 variants with bad SE.
Thu Oct 27 01:33:28 2022  -Checking STATUS...
Thu Oct 27 01:33:28 2022  -Coverting STAUTUS to category.
Thu Oct 27 01:33:28 2022  -Removed 0 variants with bad statistics in total.
Thu Oct 27 01:33:28 2022 Finished sanity check successfully!
Thu Oct 27 01:33:28 2022 Start to normalize variants...
Thu Oct 27 01:33:28 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:33:29 2022  -No available variants to normalize..
Thu Oct 27 01:33:29 2022 Finished normalizing variants successfully!
In [7]:
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mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
Thu Oct 27 01:34:28 2022 Start to perform liftover...
Thu Oct 27 01:34:28 2022  -Current Dataframe shape : 1000000  x  12
Thu Oct 27 01:34:28 2022  -CPU Cores to use : 4
Thu Oct 27 01:34:28 2022  -Performing liftover ...
Thu Oct 27 01:34:28 2022  -Creating converter : hg19 to hg38
Thu Oct 27 01:34:29 2022  -Converting variants with status code xxx0xxx :1000000...
Thu Oct 27 01:35:39 2022  -Removed unmapped variants: 619
Thu Oct 27 01:35:45 2022 Finished liftover successfully!
In [4]:
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known = pd.read_csv("t2d_known.txt")
known = pd.read_csv("t2d_known.txt")
In [5]:
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known
known
Out[5]:
SNPID CHR POS BETA SE P OR STATUS REPORT_GENENAME CLOSEST_GENENAMES TRAIT STUDY PUBMEDID
0 rs12741141 1 6609910 0.0395 0.0048 1.000000e-16 NaN 9990999 NR KLHL21,PHF13 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
1 rs11583755 1 6612669 0.0369 0.0041 1.000000e-19 NaN 9990999 NR KLHL21,PHF13 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
2 rs1010447 1 11209739 NaN NaN 2.000000e-08 NaN 9990999 MTOR RNU6-291P,ANGPTL7 Body mass index and type 2 diabetes (pairwise) Genome-wide discovery of genetic loci that unc... 33619380
3 rs4845987 1 11246222 0.0282 0.0051 3.000000e-08 NaN 9990999 NR RPL39P6,UBIAD1 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
4 rs7554251 1 11257875 0.0297 0.0045 3.000000e-11 NaN 9990999 NR RPL39P6,UBIAD1 Type 2 diabetes Discovery of 318 new risk loci for type 2 diab... 32541925
... ... ... ... ... ... ... ... ... ... ... ... ... ...
3934 rs5945326 23 153634467 NaN NaN 2.000000e-12 1.140000 9990999 DUSP9 LOC105373384,DUSP9 Type 2 diabetes Genome-wide association study identifies three... 23945395
3935 rs5945326 23 153634467 NaN NaN 3.000000e-10 1.270000 9990999 DUSP9 LOC105373384,DUSP9 Type 2 diabetes Twelve type 2 diabetes susceptibility loci ide... 20581827
3936 rs5945326 23 153634467 0.1203 0.0055 8.000000e-106 NaN 9990999 NaN LOC105373384,DUSP9 Type 2 diabetes A cross-population atlas of genetic associatio... 34594039
3937 rs1894299 23 153643433 NaN NaN 9.000000e-58 1.130000 9990999 DUSP9 LOC105373384,RPL18AP16 Type 2 diabetes Identification of 28 new susceptibility loci f... 30718926
3938 rs1894299 23 153643433 NaN NaN 2.000000e-67 0.884338 9990999 NaN LOC105373384,RPL18AP16 Type 2 diabetes Large-scale genome-wide association study in a... 32514122

3939 rows × 13 columns

In [9]:
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mysumstats.get_novel(known = known,only_novel=False)
mysumstats.get_novel(known = known,only_novel=False)
Thu Oct 27 01:35:53 2022 Start to extract lead variants...
Thu Oct 27 01:35:53 2022  -Processing 999381 variants...
Thu Oct 27 01:35:53 2022  -Significance threshold : 5e-08
Thu Oct 27 01:35:53 2022  -Sliding window size: 500  kb
Thu Oct 27 01:35:54 2022  -Found 543 significant variants in total...
Thu Oct 27 01:35:54 2022  -Identified 4 lead variants!
Thu Oct 27 01:35:54 2022 Finished extracting lead variants successfully!
Thu Oct 27 01:35:54 2022 Start to check if lead variants are known...
Thu Oct 27 01:35:54 2022  -Lead variants in known loci: 3939
Thu Oct 27 01:35:54 2022  -Checking the minimum distance between identified lead variants and provided known variants...
Thu Oct 27 01:35:54 2022  -Identified  4  known vairants in current sumstats...
Thu Oct 27 01:35:54 2022  -Identified  0  novel vairants in current sumstats...
Thu Oct 27 01:35:54 2022 Finished checking known or novel successfully!
Out[9]:
SNPID CHR POS EA NEA EAF BETA SE P N DIRECTION STATUS TCHR+POS DISTANCE_TO_KNOWN KNOWN_ID NOVEL
96739 1:22068326_A_G 1 21741833 G A 0.7550 0.0621 0.0103 1.629000e-09 191764 ++++ 3860099 1021741833 0 rs1825307 False
213860 1:51103268_T_C 1 50637596 C T 0.7953 -0.0802 0.0120 2.519000e-11 191764 ---- 3860099 1050637596 0 rs12031188 False
534095 1:154309595_TA_T 1 154337119 TA T 0.0947 -0.0915 0.0166 3.289000e-08 191764 ---- 3860399 1154337119 1 rs68062313 False
969974 2:640986_CACAT_C 2 640986 C CACAT 0.9006 -0.0946 0.0150 2.665000e-10 191764 ---- 3860399 2000640986 1 rs72156956 False
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gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"])
sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False)
sigs.fix_pos(verbose=False)
sigs.fix_chr(verbose=False)
gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"]) sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False) sigs.fix_pos(verbose=False) sigs.fix_chr(verbose=False)
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sigs.data
sigs.data
Out[147]:
SNPID CHR POS BETA SE P OR STATUS REPORT_GENENAME CLOSEST_GENENAMES TRAIT STUDY PUBMEDID
0 rs75021220 4 110737238 NaN NaN 1.000000e-25 1.400 9990999 PITX2 PITX2 Ischemic stroke (cardioembolic) Identification of additional risk loci for str... 27068588
1 rs7193343 16 72995261 NaN NaN 2.000000e-10 1.170 9990999 ZFHX3 HCCAT5 Ischemic stroke (cardioembolic) Loci associated with ischaemic stroke and its ... 26708676
2 rs2200733 4 110789013 NaN NaN 3.000000e-32 1.370 9990999 PITX2 PITX2,MIR297 Ischemic stroke (cardioembolic) Loci associated with ischaemic stroke and its ... 26708676
3 rs74475935 16 15961249 NaN NaN 5.000000e-11 4.630 9990999 ABCC1 LOC107984869 Ischemic stroke (undetermined subtype) Loci associated with ischaemic stroke and its ... 26708676
4 rs10744777 12 111795214 NaN NaN 3.000000e-09 1.170 9990999 ALDH2 MIR6761,ACAD10 Ischemic stroke (small artery occlusion) Loci associated with ischaemic stroke and its ... 26708676
... ... ... ... ... ... ... ... ... ... ... ... ... ...
193 rs11880613 19 10793296 0.0613 0.011 3.000000e-08 NaN 9990999 None MIR4748,MIR199A1 Ischemic stroke A cross-population atlas of genetic associatio... 34594039
194 rs3897976 3 41565201 NaN NaN 3.000000e-08 2.162 9990999 None ALCAM Ischemic stroke in dyslipidemia Identification of susceptibility loci for card... 33632238
195 rs149608518 4 164551523 NaN NaN 1.000000e-08 5.587 9990999 None RNU6-284P Ischemic stroke in diabetes mellitus Identification of susceptibility loci for card... 33632238
196 rs189668056 2 38081685 NaN NaN 4.000000e-08 2.027 9990999 None CYP1B1,LOC105374466 Cardio-cerebrovascular disease in dyslipidemia Identification of susceptibility loci for card... 33632238
197 rs139293840 17 80556559 NaN NaN 2.000000e-08 3.511 9990999 None RPL32P31,LOC105371922 Cardio-cerebrovascular disease in diabetes mel... Identification of susceptibility loci for card... 33632238

198 rows × 13 columns

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locations = pd.json_normalize(api_response["_embedded"]["associations"],"snps",errors='ignore')[["locations","genomicContexts"]]
locations = pd.json_normalize(api_response["_embedded"]["associations"],"snps",errors='ignore')[["locations","genomicContexts"]]
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Out[135]:
locations genomicContexts
0 [{'chromosomeName': '8', 'chromosomePosition':... [{'isIntergenic': False, 'isUpstream': False, ...
1 [{'chromosomeName': '19', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': True, 'i...
2 [{'chromosomeName': '8', 'chromosomePosition':... [{'isIntergenic': True, 'isUpstream': False, '...
3 [{'chromosomeName': '11', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': True, 'i...
4 [{'chromosomeName': '1', 'chromosomePosition':... [{'isIntergenic': True, 'isUpstream': True, 'i...
... ... ...
68 [{'chromosomeName': '19', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': False, '...
69 [{'chromosomeName': '3', 'chromosomePosition':... [{'isIntergenic': True, 'isUpstream': True, 'i...
70 [{'chromosomeName': '19', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': True, 'i...
71 [{'chromosomeName': 'CHR_HSCHR6_MHC_DBB_CTG1',... [{'isIntergenic': True, 'isUpstream': True, 'i...
72 [{'chromosomeName': 'CHR_HSCHR6_MHC_MCF_CTG1',... [{'isIntergenic': True, 'isUpstream': False, '...

73 rows × 2 columns

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layer1 = pd.json_normalize(api_response["_embedded"]["associations"])
layer1
layer1 = pd.json_normalize(api_response["_embedded"]["associations"]) layer1
Out[77]:
range snps loci riskFrequency pvalueDescription orPerCopyNum snpType multiSnpHaplotype snpInteraction pvalueMantissa ... study.publicationInfo.title study.publicationInfo.author.fullname study.publicationInfo.author.orcid _links.self.href _links.association.href _links.association.templated _links.snps.href _links.backgroundEfoTraits.href _links.study.href _links.efoTraits.href
0 [1.65-2.5] [{'rsId': 'rs12678747', 'merged': 0, 'function... [{'haplotypeSnpCount': None, 'description': 'S... NR None 2.03 novel False False 3 ... Genome-Wide association between EYA1 and Aspir... Bourgeois S None https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
1 NR [{'rsId': 'rs681343', 'merged': 0, 'functional... [{'haplotypeSnpCount': None, 'description': 'S... 0.49 None 0.92 novel False False 2 ... GWAS of peptic ulcer disease implicates Helico... Wu Y 0000-0002-5977-1526 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
2 NR [{'rsId': 'rs2976388', 'merged': 0, 'functiona... [{'haplotypeSnpCount': None, 'description': 'S... 0.58 None 1.09 novel False False 2 ... GWAS of peptic ulcer disease implicates Helico... Wu Y 0000-0002-5977-1526 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
3 NR [{'rsId': 'rs10500661', 'merged': 0, 'function... [{'haplotypeSnpCount': None, 'description': 'S... 0.8 None 0.90 novel False False 4 ... GWAS of peptic ulcer disease implicates Helico... Wu Y 0000-0002-5977-1526 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
4 NR [{'rsId': 'rs147048677', 'merged': 0, 'functio... [{'haplotypeSnpCount': None, 'description': 'S... 0.94 None 0.86 novel False False 9 ... GWAS of peptic ulcer disease implicates Helico... Wu Y 0000-0002-5977-1526 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
68 None [{'rsId': 'rs11083749', 'merged': 0, 'function... [{'haplotypeSnpCount': None, 'description': 'S... NR None NaN novel False False 3 ... A large-scale genome-wide cross-trait analysis... Adewuyi EO 0000-0002-4533-0340 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
69 None [{'rsId': 'rs709210', 'merged': 0, 'functional... [{'haplotypeSnpCount': None, 'description': 'S... NR None NaN novel False False 4 ... A large-scale genome-wide cross-trait analysis... Adewuyi EO 0000-0002-4533-0340 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
70 None [{'rsId': 'rs11880948', 'merged': 0, 'function... [{'haplotypeSnpCount': None, 'description': 'S... NR None NaN novel False False 6 ... A large-scale genome-wide cross-trait analysis... Adewuyi EO 0000-0002-4533-0340 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
71 None [{'rsId': 'rs28732222', 'merged': 0, 'function... [{'haplotypeSnpCount': None, 'description': 'S... NR None NaN novel False False 1 ... A large-scale genome-wide cross-trait analysis... Adewuyi EO 0000-0002-4533-0340 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...
72 None [{'rsId': 'rs17206350', 'merged': 0, 'function... [{'haplotypeSnpCount': None, 'description': 'S... NR None NaN novel False False 1 ... A large-scale genome-wide cross-trait analysis... Adewuyi EO 0000-0002-4533-0340 https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... True https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio... https://www.ebi.ac.uk/gwas/rest/api/associatio...

73 rows × 46 columns

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layer2 = pd.json_normalize(api_response["_embedded"]["associations"],"snps")
layer2
layer2 = pd.json_normalize(api_response["_embedded"]["associations"],"snps") layer2
Out[78]:
rsId merged functionalClass lastUpdateDate locations genomicContexts
0 rs12678747 0 intron_variant 2022-03-23T17:19:52.947+0000 [{'chromosomeName': '8', 'chromosomePosition':... [{'isIntergenic': False, 'isUpstream': False, ...
1 rs681343 0 stop_gained 2022-08-03T16:59:51.731+0000 [{'chromosomeName': '19', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': True, 'i...
2 rs2976388 0 intron_variant 2021-06-24T21:12:27.021+0000 [{'chromosomeName': '8', 'chromosomePosition':... [{'isIntergenic': True, 'isUpstream': False, '...
3 rs10500661 0 intergenic_variant 2021-06-25T04:18:24.804+0000 [{'chromosomeName': '11', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': True, 'i...
4 rs147048677 0 synonymous_variant 2021-06-24T21:12:28.862+0000 [{'chromosomeName': '1', 'chromosomePosition':... [{'isIntergenic': True, 'isUpstream': True, 'i...
... ... ... ... ... ... ...
68 rs11083749 0 intron_variant 2022-09-09T17:04:12.767+0000 [{'chromosomeName': '19', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': False, '...
69 rs709210 0 missense_variant 2022-09-09T17:04:14.640+0000 [{'chromosomeName': '3', 'chromosomePosition':... [{'isIntergenic': True, 'isUpstream': True, 'i...
70 rs11880948 0 intron_variant 2022-09-09T17:04:14.970+0000 [{'chromosomeName': '19', 'chromosomePosition'... [{'isIntergenic': True, 'isUpstream': True, 'i...
71 rs28732222 0 downstream_gene_variant 2022-09-09T17:04:19.712+0000 [{'chromosomeName': 'CHR_HSCHR6_MHC_DBB_CTG1',... [{'isIntergenic': True, 'isUpstream': True, 'i...
72 rs17206350 0 upstream_gene_variant 2022-09-09T17:04:24.164+0000 [{'chromosomeName': 'CHR_HSCHR6_MHC_MCF_CTG1',... [{'isIntergenic': True, 'isUpstream': False, '...

73 rows × 6 columns

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layer3 = pd.json_normalize(api_response["_embedded"]["associations"],["snps","locations"])
layer3
layer3 = pd.json_normalize(api_response["_embedded"]["associations"],["snps","locations"]) layer3
Out[80]:
chromosomeName chromosomePosition region.name _links.snps _links.snps.href _links.snps.templated
0 8 71202541 8q13.3 [{'href': 'https://www.ebi.ac.uk/gwas/rest/api... NaN NaN
1 8 71202541 8q13.3 [{'href': 'https://www.ebi.ac.uk/gwas/rest/api... NaN NaN
2 19 48703205 19q13.33 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
3 8 142678838 8q24.3 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
4 11 6252514 11p15.4 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
... ... ... ... ... ... ...
107 6 32707290 6p21.32 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
108 CHR_HSCHR6_MHC_DBB_CTG1 32686300 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
109 CHR_HSCHR6_MHC_COX_CTG1 32630720 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
110 CHR_HSCHR6_MHC_QBL_CTG1 32635972 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
111 CHR_HSCHR6_MHC_SSTO_CTG1 32799385 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True

112 rows × 6 columns

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layer3.drop_duplicates(subset=["chromosomeName","chromosomePosition"])
layer3.drop_duplicates(subset=["chromosomeName","chromosomePosition"])
Out[82]:
chromosomeName chromosomePosition region.name _links.snps _links.snps.href _links.snps.templated
0 8 71202541 8q13.3 [{'href': 'https://www.ebi.ac.uk/gwas/rest/api... NaN NaN
2 19 48703205 19q13.33 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
3 8 142678838 8q24.3 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
4 11 6252514 11p15.4 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
5 1 155192003 1q22 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
... ... ... ... ... ... ...
107 6 32707290 6p21.32 NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
108 CHR_HSCHR6_MHC_DBB_CTG1 32686300 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
109 CHR_HSCHR6_MHC_COX_CTG1 32630720 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
110 CHR_HSCHR6_MHC_QBL_CTG1 32635972 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True
111 CHR_HSCHR6_MHC_SSTO_CTG1 32799385 None NaN https://www.ebi.ac.uk/gwas/rest/api/singleNucl... True

109 rows × 6 columns

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for i in api_response["_embedded"]["associations"]:
    if "pvalue" in i:
        if float(i["pvalue"])<5e-8:      
            snp = pd.json_normalize(api_response["_embedded"]["associations"][0]["snps"],max_level=0)

            
            
            if "rsId" in i["snps"][0]:
                print(i["snps"][0]["rsId"], end=",")
                if "locations" in i["snps"][0]:
                    if len(i["snps"][0]["locations"])>0:
                        print(i["snps"][0]["locations"][0]["chromosomeName"],end=" ")
                    if len(i["snps"][0]["locations"])>0:
                        print(i["snps"][0]["locations"][0]["chromosomePosition"],end=" ")   
                if "genomicContexts" in i["snps"][0]:
                    if "gene" in i["snps"][0]["genomicContexts"][0]:
                        if "geneName" in i["snps"][0]["genomicContexts"][0]["gene"]:
                            print(i["snps"][0]["genomicContexts"][0]["gene"]["geneName"])
            print(i["pvalue"])
for i in api_response["_embedded"]["associations"]: if "pvalue" in i: if float(i["pvalue"])<5e-8: snp = pd.json_normalize(api_response["_embedded"]["associations"][0]["snps"],max_level=0) if "rsId" in i["snps"][0]: print(i["snps"][0]["rsId"], end=",") if "locations" in i["snps"][0]: if len(i["snps"][0]["locations"])>0: print(i["snps"][0]["locations"][0]["chromosomeName"],end=" ") if len(i["snps"][0]["locations"])>0: print(i["snps"][0]["locations"][0]["chromosomePosition"],end=" ") if "genomicContexts" in i["snps"][0]: if "gene" in i["snps"][0]["genomicContexts"][0]: if "geneName" in i["snps"][0]["genomicContexts"][0]["gene"]: print(i["snps"][0]["genomicContexts"][0]["gene"]["geneName"]) print(i["pvalue"])
rs12678747,8 71202541 EYA1
3e-11
rs681343,19 48703205 FAM83E
2e-15
rs2976388,8 142678838 SLURP2
2e-14
rs10500661,11 6252514 OR52B2
4e-14
rs147048677,1 155192003 HMGN2P18
9e-12
rs78459074,CHR_HSCHR11_2_CTG1 1036727 AP2A2
3e-10
rs34074411,17 41710996 GAST
3e-10
rs687621,9 133261662 MED22
1e-09
rs9581957,13 27983752 CDX2
4e-09
rs200964,6 27899165 H4C11
3.0000000000000003e-13
rs967823,17 52239916 CA10
2e-12
chr19:18793695,
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-41-786e8dc656a6> in <module>
     10                         print(i["snps"][0]["locations"][0]["chromosomePosition"],end=" ")
     11                 if "genomicContexts" in i["snps"][0]:
---> 12                     if "gene" in i["snps"][0]["genomicContexts"][0]:
     13                         if "geneName" in i["snps"][0]["genomicContexts"][0]["gene"]:
     14                             print(i["snps"][0]["genomicContexts"][0]["gene"]["geneName"])

IndexError: list index out of range
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for item,associations in api_response["_embedded"].items():
    associations[0]["snp"][0]["rsID"]
for item,associations in api_response["_embedded"].items(): associations[0]["snp"][0]["rsID"]
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import re
pattern = re.compile(r'rs[0-9]+')
import re pattern = re.compile(r'rs[0-9]+')
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a=pattern.search("'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs17206350{?projection}'")
a[0]
a=pattern.search("'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs17206350{?projection}'") a[0]
rs17206350
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for value in api_response["_embedded"].values():
    for i in value:
        a=pattern.search(i['loci'][0]["strongestRiskAlleles"][0]["_links"]["snp"]["href"])
        if a is None:
            continue
        base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/"+a[0]
        r = requests.get(base_url)
        snp_response = json.loads(r.text)
        print(a[0],snp_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
for value in api_response["_embedded"].values(): for i in value: a=pattern.search(i['loci'][0]["strongestRiskAlleles"][0]["_links"]["snp"]["href"]) if a is None: continue base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/"+a[0] r = requests.get(base_url) snp_response = json.loads(r.text) print(a[0],snp_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-55-257d03c020b1> in <module>
----> 1 for value in api_response["_embedded"].values():
      2     for i in value:
      3         a=pattern.search(i['loci'][0]["strongestRiskAlleles"][0]["_links"]["snp"]["href"])
      4         if a is None:
      5             continue

KeyError: '_embedded'
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base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs3852865"

# Perform POST request and check status code of response
r = requests.get(base_url)
print(r.status_code)

# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
print(api_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs3852865" # Perform POST request and check status code of response r = requests.get(base_url) print(r.status_code) # Transform API response from JSON into Python dictionary and print in console api_response = json.loads(r.text) print(api_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
200
19 51210809
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